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VCFX_cross_sample_concordance

Overview

VCFX_cross_sample_concordance analyzes a multi-sample VCF file to determine if genotypes are consistent across all samples for each variant. It identifies variants where samples show concordance (agreement) or discordance (disagreement) in their genotype calls.

Usage

VCFX_cross_sample_concordance [OPTIONS] < input.vcf > concordance_results.tsv

Options

Option Description
-h, --help Display help message and exit (handled by vcfx::handle_common_flags)
-v, --version Show program version and exit (handled by vcfx::handle_common_flags)
-s, --samples Comma-separated list of samples to check

Description

VCFX_cross_sample_concordance examines each variant in a multi-sample VCF file and determines if all samples with valid genotypes have the same normalized genotype. The tool:

  1. Normalizes genotypes across samples by:
  2. Converting phased genotypes (|) to unphased (/)
  3. Handling multi-allelic variants properly
  4. Sorting alleles numerically for consistent comparison (e.g., 1/0 becomes 0/1)
  5. Compares the normalized genotypes across all samples for each variant
  6. Classifies each variant as:
  7. CONCORDANT: All samples with valid genotypes have the same normalized genotype
  8. DISCORDANT: Samples have different normalized genotypes
  9. NO_GENOTYPES: No samples have valid genotypes for this variant
  10. Outputs detailed per-variant results to standard output
  11. Provides a summary of concordance statistics to standard error

This tool is particularly useful for: - Quality control of multi-sample VCF files - Identifying potential sample mix-ups or contamination - Validating genotype calling consistency across technical replicates - Assessing reliability of variant calls across different sequencing or analysis methods

Output Format

The tool produces a tab-separated values (TSV) file with the following columns:

Column Description
CHROM Chromosome of the variant
POS Position of the variant
ID Variant identifier
REF Reference allele
ALT Alternate allele(s)
Num_Samples Number of samples with valid genotypes
Unique_Normalized_Genotypes Number of distinct normalized genotypes observed
Concordance_Status Status: CONCORDANT, DISCORDANT, or NO_GENOTYPES

Additionally, a summary of statistics is printed to standard error, including: - Total number of variants processed - Number of concordant variants - Number of discordant variants - Number of variants with no valid genotypes

Examples

Basic Usage

Check concordance in a multi-sample VCF file: 

VCFX_cross_sample_concordance < input.vcf > concordance_results.tsv

Specify a subset of samples:

VCFX_cross_sample_concordance --samples SampleA,SampleB < input.vcf > concordance_subset.tsv

Filtering for Discordant Variants

Identify only variants with discordant genotypes: 

VCFX_cross_sample_concordance < input.vcf | grep "DISCORDANT" > discordant_variants.tsv

Concordance Analysis in a Pipeline

Use as part of a larger analysis pipeline: 

cat input.vcf | VCFX_cross_sample_concordance | awk -F'\t' '{if($8=="CONCORDANT") print $0}' > consistent_variants.tsv

Saving Both Results and Summary

Capture both the detailed results and summary statistics: 

VCFX_cross_sample_concordance < input.vcf > concordance_results.tsv 2> concordance_summary.txt

Genotype Normalization

Process

For each sample's genotype, the tool performs the following normalization steps: 1. Extracts the genotype field (first field in the FORMAT column) 2. Converts all phase separators (|) to unphased separators (/) 3. Splits the genotype into individual allele indices 4. Validates each allele (skips if missing or invalid) 5. Sorts allele indices in ascending order (e.g., 1/0 → 0/1) 6. Rejoins the allele indices with / separators

Example Normalizations

  • 0|1 → 0/1
  • 1/0 → 0/1
  • 1|2 → 1/2
  • 2/1 → 1/2
  • ./1 → (skipped as invalid)
  • 0/0 → 0/0 (unchanged)

Handling Special Cases

Missing Genotypes

  • Genotypes with missing values (./., .) are excluded from concordance calculation
  • If no samples have valid genotypes for a variant, it is classified as NO_GENOTYPES

Multi-allelic Variants

  • Alt alleles are parsed from the ALT column (comma-separated)
  • Genotype allele indices are validated against the number of alt alleles
  • Invalid indices (exceeding the number of alt alleles) are treated as missing

Phased Genotypes

  • Phasing information is ignored for concordance calculation
  • Genotypes that differ only in phasing are considered concordant

Malformed VCF Lines

  • Lines with insufficient columns are skipped
  • Lines encountered before the #CHROM header are skipped with a warning
  • Genotypes that cannot be parsed are treated as missing

Performance Considerations

  • Processes the VCF file line by line, requiring minimal memory
  • Time complexity scales linearly with file size and number of samples
  • Efficient handling of large multi-sample VCF files with normalized genotype comparisons
  • No file indexing or preprocessing required

Limitations

  • Only handles diploid genotypes (e.g., 0/1, not haploid 0 or polyploid genotypes)
  • Ignores genotype phasing information in concordance assessment
  • Does not consider genotype quality or other FORMAT fields in the assessment
  • No option to adjust concordance thresholds (e.g., requiring 90% sample agreement)
  • Cannot output detailed per-sample information for discordant variants